Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009643.1 Hibiscus syriacus cultivar Beakdansim tig00117056_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8859806
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 41
Found at i:3671376 original size:164 final size:163
Alignment explanation
Indices: 3671105--3671429 Score: 483
Period size: 164 Copynumber: 2.0 Consensus size: 163
3671095 TTATATTATC
* * *
3671105 TCTAACATTTATTATCTTTATTTTCTATTTTGACTTGGAATTCTCCTGTAATTTGGTTCCATTAA
1 TCTAACATTTATTATCTTTATTTTCTATTTTGACTTGG-ACTCTCCAGTAATTTGCTTCCATTAA
* * * * * *
3671170 TTTGTGCAGGCACTACTGGGGTATGATAAGCATAAAATGCATGGTGTTGTACTCCCTCGTTCCGT
65 TTTGTGCAGGCACTACTGGGGTATGACAAGCATAAAATGCATGGCGCTATACTACCTCATTCCGT
*
3671235 TCCTTCCCTCATAGGGCCTTTCACAGTTGTTGTT
130 TCCTTCCCTCATAAGGCCTTTCACAGTTGTTGTT
3671269 TCTAACATTTATTATCTTTATTTTCTATTTTGACATGTGG-CTCTCCAGTAATTTGCTTCCATTA
1 TCTAACATTTATTATCTTTATTTTCTATTTTGAC-T-TGGACTCTCCAGTAATTTGCTTCCATTA
* * *
3671333 ATTTGTGCATGCGCTTA-TGGGGTATGACAAGCATAAAATGCATGGCGCTATACTACCTCATTTC
64 ATTTGTGCAGGCAC-TACTGGGGTATGACAAGCATAAAATGCATGGCGCTATACTACCTCATTCC
3671397 GTTCCTTCCCTCATAAGGCCTTTCACAGTTGTT
128 GTTCCTTCCCTCATAAGGCCTTTCACAGTTGTT
3671430 TGTCTGGTAA
Statistics
Matches: 145, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
164 139 0.96
165 3 0.02
166 3 0.02
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (163 bp):
TCTAACATTTATTATCTTTATTTTCTATTTTGACTTGGACTCTCCAGTAATTTGCTTCCATTAAT
TTGTGCAGGCACTACTGGGGTATGACAAGCATAAAATGCATGGCGCTATACTACCTCATTCCGTT
CCTTCCCTCATAAGGCCTTTCACAGTTGTTGTT
Found at i:3677518 original size:3 final size:3
Alignment explanation
Indices: 3677512--3677546 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
3677502 CTCCATTTAC
3677512 TAT TAT TATT TAT TAT TAT TAT TAT TAT T-T TAT TA
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TA
3677547 CAAACGGGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:3677528 original size:13 final size:13
Alignment explanation
Indices: 3677506--3677545 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
3677496 TTTTTTCTCC
*
3677506 ATTTACTATTATT
1 ATTTATTATTATT
3677519 ATTTATTATTATT
1 ATTTATTATTATT
3677532 A-TTATTATT-TT
1 ATTTATTATTATT
3677543 ATT
1 ATT
3677546 ACAAACGGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 3 0.12
12 9 0.36
13 13 0.52
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTATTATTATT
Found at i:3683019 original size:15 final size:15
Alignment explanation
Indices: 3683001--3683032 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3682991 GATCAATACC
3683001 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
3683016 TTTTGCATACATTCA
1 TTTTGCATACATGCA
3683031 TT
1 TT
3683033 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:3691542 original size:93 final size:93
Alignment explanation
Indices: 3691383--3691567 Score: 327
Period size: 93 Copynumber: 2.0 Consensus size: 93
3691373 GACCCAATAG
*
3691383 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCTAAAAACCAATCAT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGAACTGGTTTGGTATGAACCCTAAAAACCAATCAT
*
3691448 TGAATTTGGAAGATGAATGTGCTCATAT
66 TGAATTTGAAAGATGAATGTGCTCATAT
3691476 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGAACTGGTTTGGTATGAACCAC-AAAAACCAATCA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGAACTGGTTTGGTATGAACC-CTAAAAACCAATCA
*
3691540 TTGGATTTGAAAGATGAATGTGCTCATA
65 TTGAATTTGAAAGATGAATGTGCTCATA
3691568 GTAGAAATAA
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
93 87 0.99
94 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (93 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGAACTGGTTTGGTATGAACCCTAAAAACCAATCAT
TGAATTTGAAAGATGAATGTGCTCATAT
Found at i:3692695 original size:113 final size:111
Alignment explanation
Indices: 3692350--3692912 Score: 643
Period size: 113 Copynumber: 5.0 Consensus size: 111
3692340 TAGCAAAGAT
* * * * *
3692350 TCAAATCCATCAATTGATGGATCAACATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGA
1 TCAAATCCATC-ATTGATGGATCAGCATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTAA
*
3692415 AGAAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCCACCTTTTGC
65 AGAA-GAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
3692463 TCAAATCCATCAATTGATGGATCAGTATTGA-CAGGTAGAGTTCATAATGAGAAGAACTCGTC-A
1 TCAAATCCATC-ATTGATGGATCAGCATT-ACCAGATAGAGTTCATAATGAGAAGAACTCATCTA
** * * *
3692526 TCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGC
64 -AAGAAGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
3692575 TCCAATTCATCATTCAATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTAA
1 TCAAATCCATCATT-GATGGATCAGCATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTAA
*
3692640 AGAAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
65 AGAA-GAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * * *
3692688 TTGAATTCATCATTTGATGGATCAACATTGCCAGATAAAGTTCATAATGAGAAGAACTTGTCATC
1 TCAAATCCATCA-TTGATGGATCAGCATTACCAGATAGAGTTCATAATGAGAAGAAC---TCATC
* *
3692753 TGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
62 TAAAGAAGAAA-AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
3692804 T-AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT--
1 TCAAATCCATCA-TTGATGGATCAGCATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTAA
* **
3692866 -GAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCCTTTTGC
65 AGAAGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CCTTTTGC
3692913 ATAATTCTAT
Statistics
Matches: 390, Mismatches: 48, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
108 28 0.07
109 14 0.04
111 4 0.01
112 97 0.25
113 143 0.37
114 3 0.01
115 52 0.13
116 49 0.13
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (111 bp):
TCAAATCCATCATTGATGGATCAGCATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTAAA
GAAGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:3692757 original size:225 final size:225
Alignment explanation
Indices: 3692352--3692912 Score: 756
Period size: 225 Copynumber: 2.5 Consensus size: 225
3692342 GCAAAGATTC
* * * *
3692352 AAATCCATCAATTGATGGATCAACATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTAATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCT-AAG
*
3692417 AAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCCACCTTTTGCTCAAATCCATCAATTGATG
65 AAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCAATTGATG
** * *
3692482 GATCAGTATTGACAGGTAGAGTTCATAATGAGAAGAACTCGTCATCT-GAAG-AAGAAGAAATTC
130 GATCAACATTGACAGATAAAGTTCATAATGAGAAGAACTCGTCATCTAGAAGAAAGAAGAAATTC
*
3692545 ATAATGAGAAGAATTTGTTCAACTTTTTGCT
195 ATAATGAGAAGAATTTGTTCAACCTTTTGCT
* *
3692576 CCAATTCATCA-TTCAATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTAA
1 -AAATCCATCACTT-AATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCT-A
* ** * *
3692640 AGAAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGA
63 AGAAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCAATTGA
* *
3692705 TGGATCAACATTGCCAGATAAAGTTCATAATGAGAAGAACTTGTCATCTGAAGAAGAAAGAAGAA
128 TGGATCAACATTGACAGATAAAGTTCATAATGAGAAGAACTCGTCATCT--AGAAGAAAGAAGAA
3692770 ATTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
191 ATTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
* * * ****
3692805 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT--GA
1 AAATCCATCACTTAATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTAAGA
* **
3692868 A-GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCCTTTTGC
66 AGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CCTTTTGC
3692913 ATAATTCTAT
Statistics
Matches: 297, Mismatches: 32, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
224 34 0.11
225 166 0.56
228 53 0.18
229 44 0.15
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (225 bp):
AAATCCATCACTTAATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTAAGA
AGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCAATTGATGG
ATCAACATTGACAGATAAAGTTCATAATGAGAAGAACTCGTCATCTAGAAGAAAGAAGAAATTCA
TAATGAGAAGAATTTGTTCAACCTTTTGCT
Found at i:3693271 original size:3 final size:3
Alignment explanation
Indices: 3693265--3693317 Score: 88
Period size: 3 Copynumber: 17.0 Consensus size: 3
3693255 CTCCATTTAC
3693265 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
3693312 TAT TAT
1 TAT TAT
3693318 AAACGGGCCA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 42 0.88
4 6 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3699206 original size:15 final size:16
Alignment explanation
Indices: 3699188--3699221 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3699178 CCTTTTCATC
*
3699188 TATAATTAT-TTATTT
1 TATAAATATATTATTT
3699203 TATAAATATATTATTT
1 TATAAATATATTATTT
3699219 TAT
1 TAT
3699222 TTTATTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAAATATATTATTT
Found at i:3699969 original size:2 final size:2
Alignment explanation
Indices: 3699962--3699999 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3699952 TTCACGCACT
3699962 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3700000 GAAATTGACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3703323 original size:15 final size:15
Alignment explanation
Indices: 3703305--3703335 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3703295 CACAATAAGA
3703305 AACCCACATAATCAC
1 AACCCACATAATCAC
3703320 AACCCACATAATCAC
1 AACCCACATAATCAC
3703335 A
1 A
3703336 CGGCAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.39, G:0.00, T:0.13
Consensus pattern (15 bp):
AACCCACATAATCAC
Found at i:3714763 original size:2 final size:2
Alignment explanation
Indices: 3714756--3714787 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3714746 TTACTATTAA
3714756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3714788 TTAATTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3719597 original size:76 final size:76
Alignment explanation
Indices: 3719507--3719660 Score: 245
Period size: 76 Copynumber: 2.0 Consensus size: 76
3719497 ACTTATAAAA
* * * * *
3719507 AAATATGTATTCTTTTTTAAATATAATATTTAATATATTAATCAATTAATTCTGATTAGATTTTA
1 AAATACGTATTCTTTTATAAATATAATATTTAATATATTAATCAATTAATTCTAATTAAATATTA
3719572 TAAAAACTCAT
66 TAAAAACTCAT
* *
3719583 AAATACGTATTCTTTTATAAATATGATATTTAATATATTAATCAATTAATTTTAATTAAATATTA
1 AAATACGTATTCTTTTATAAATATAATATTTAATATATTAATCAATTAATTCTAATTAAATATTA
3719648 TAAAAACTCAT
66 TAAAAACTCAT
3719659 AA
1 AA
3719661 GATGTGATTA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (76 bp):
AAATACGTATTCTTTTATAAATATAATATTTAATATATTAATCAATTAATTCTAATTAAATATTA
TAAAAACTCAT
Found at i:3720189 original size:2 final size:2
Alignment explanation
Indices: 3720182--3720259 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
3720172 ACTAAAAATC
3720182 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3720224 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3720260 CATGAAGGTG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3736436 original size:22 final size:22
Alignment explanation
Indices: 3736408--3736461 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
3736398 TATTATTATT
3736408 TTTAATAATTATTGTATTTGAA
1 TTTAATAATTATTGTATTTGAA
3736430 TTTAATAATTATTGTATTTGAA
1 TTTAATAATTATTGTATTTGAA
3736452 TTTAATAATT
1 TTTAATAATT
3736462 GATTAGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (22 bp):
TTTAATAATTATTGTATTTGAA
Found at i:3740943 original size:35 final size:35
Alignment explanation
Indices: 3740897--3740972 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
3740887 AACATAGTCC
* *
3740897 TCAATTTTATTTTAAACCCTAAATTCCAAAATAAT
1 TCAATTATATTTTAAACCCCAAATTCCAAAATAAT
* * *
3740932 TCAATTATATTTTAAGCCCCAAATTCTAAAATACT
1 TCAATTATATTTTAAACCCCAAATTCCAAAATAAT
3740967 TCAATT
1 TCAATT
3740973 TGGGGTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.18, G:0.01, T:0.39
Consensus pattern (35 bp):
TCAATTATATTTTAAACCCCAAATTCCAAAATAAT
Found at i:3741010 original size:35 final size:35
Alignment explanation
Indices: 3740969--3741043 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
3740959 AAAATACTTC
3740969 AATTTGGGGTTTAAAATGTAATTAAAATATTTTGG
1 AATTTGGGGTTTAAAATGTAATTAAAATATTTTGG
* * * *
3741004 AATTTGGGGTTTAGAATGTAATTGAAGTGTTTTGG
1 AATTTGGGGTTTAAAATGTAATTAAAATATTTTGG
3741039 AATTT
1 AATTT
3741044 TGAACATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (35 bp):
AATTTGGGGTTTAAAATGTAATTAAAATATTTTGG
Found at i:3743703 original size:2 final size:2
Alignment explanation
Indices: 3743696--3743722 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3743686 TCTCTAATCG
3743696 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3743723 GTTAGGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3744419 original size:20 final size:20
Alignment explanation
Indices: 3744382--3744422 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3744372 TACTAGCTGT
**
3744382 TGCAGGGTGTATGGATACAC
1 TGCAGGGTGTATCAATACAC
3744402 TGCAGGGTGTATCAATACAC
1 TGCAGGGTGTATCAATACAC
3744422 T
1 T
3744423 AGTGTATGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (20 bp):
TGCAGGGTGTATCAATACAC
Found at i:3744435 original size:16 final size:18
Alignment explanation
Indices: 3744387--3744458 Score: 51
Period size: 20 Copynumber: 3.9 Consensus size: 18
3744377 GCTGTTGCAG
3744387 GGTGTATGGATACACTGCA
1 GGTGTATGGATACACT-CA
**
3744406 GGGTGTATCAATACACT-A
1 -GGTGTATGGATACACTCA
*
3744424 -GTGTATGGATACAATCATA
1 GGTGTATGGATACACTC--A
3744443 GGTGTATCGG-TACACT
1 GGTGTAT-GGATACACT
3744459 ATTTGCATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
16 12 0.29
18 1 0.02
19 1 0.02
20 25 0.61
21 2 0.05
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (18 bp):
GGTGTATGGATACACTCA
Found at i:3744447 original size:36 final size:36
Alignment explanation
Indices: 3744388--3744459 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
3744378 CTGTTGCAGG
* *
3744388 GTGTATGGATACACTGCAGGGTGTATCAATACACTA
1 GTGTATGGATACAATGCAAGGTGTATCAATACACTA
**
3744424 GTGTATGGATACAAT-CATAGGTGTATCGGTACACTA
1 GTGTATGGATACAATGCA-AGGTGTATCAATACACTA
3744460 TTTGCATTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 2 0.06
36 29 0.94
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (36 bp):
GTGTATGGATACAATGCAAGGTGTATCAATACACTA
Found at i:3744530 original size:16 final size:16
Alignment explanation
Indices: 3744509--3744539 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3744499 CACTTGCAGG
*
3744509 GTGTATTGATACACTA
1 GTGTATGGATACACTA
3744525 GTGTATGGATACACT
1 GTGTATGGATACACT
3744540 GCAGGGTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (16 bp):
GTGTATGGATACACTA
Found at i:3748503 original size:19 final size:19
Alignment explanation
Indices: 3748479--3748527 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
3748469 GAATGCAATT
3748479 AGTGCATCGATGCATGATG
1 AGTGCATCGATGCATGATG
3748498 AGTGCATCGATGCATGATG
1 AGTGCATCGATGCATGATG
3748517 AGTGCATCGAT
1 AGTGCATCGAT
3748528 ACACCCACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (19 bp):
AGTGCATCGATGCATGATG
Found at i:3748595 original size:24 final size:24
Alignment explanation
Indices: 3748568--3748648 Score: 153
Period size: 24 Copynumber: 3.4 Consensus size: 24
3748558 AAATTGTGTT
3748568 TCGATGCACATGTTAAAGAGTGCA
1 TCGATGCACATGTTAAAGAGTGCA
3748592 TCGATGCACATGTTAAAGAGTGCA
1 TCGATGCACATGTTAAAGAGTGCA
*
3748616 TCGATGCACATATTAAAGAGTGCA
1 TCGATGCACATGTTAAAGAGTGCA
3748640 TCGATGCAC
1 TCGATGCAC
3748649 TGTAGTATGT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (24 bp):
TCGATGCACATGTTAAAGAGTGCA
Found at i:3749438 original size:18 final size:18
Alignment explanation
Indices: 3749415--3749484 Score: 122
Period size: 18 Copynumber: 3.9 Consensus size: 18
3749405 TGTGTTCTAT
3749415 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
3749433 GTGGTCCTTCAGGACATA
1 GTGGTCCTTCGGGACATA
3749451 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
3749469 GTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACA
3749485 AATTTCTACG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.19, C:0.23, G:0.33, T:0.26
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:3752777 original size:19 final size:19
Alignment explanation
Indices: 3752753--3752820 Score: 136
Period size: 19 Copynumber: 3.6 Consensus size: 19
3752743 GAATGCAATT
3752753 AGTGCATCGATGCATGATG
1 AGTGCATCGATGCATGATG
3752772 AGTGCATCGATGCATGATG
1 AGTGCATCGATGCATGATG
3752791 AGTGCATCGATGCATGATG
1 AGTGCATCGATGCATGATG
3752810 AGTGCATCGAT
1 AGTGCATCGAT
3752821 ACACCCCCTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.26
Consensus pattern (19 bp):
AGTGCATCGATGCATGATG
Found at i:3753756 original size:18 final size:18
Alignment explanation
Indices: 3753687--3753748 Score: 99
Period size: 18 Copynumber: 3.4 Consensus size: 18
3753677 TGTGTTCTAT
3753687 GTGGTCCTTC-GAGACATA
1 GTGGTCCTTCAG-GACATA
*
3753705 GTGGTCCTTCATGACATA
1 GTGGTCCTTCAGGACATA
3753723 GTGGTCCTTCAGGACATA
1 GTGGTCCTTCAGGACATA
3753741 GTGGTCCT
1 GTGGTCCT
3753749 ACGGGACAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (18 bp):
GTGGTCCTTCAGGACATA
Found at i:3754633 original size:21 final size:21
Alignment explanation
Indices: 3754607--3754660 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
3754597 CCATAACAAG
*
3754607 GTGTATCGGTACACTATCAAA
1 GTGTATCGATACACTATCAAA
3754628 GTGTATCGATACACTATCAAA
1 GTGTATCGATACACTATCAAA
3754649 GTGTATCGATAC
1 GTGTATCGATAC
3754661 CCCTTCATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (21 bp):
GTGTATCGATACACTATCAAA
Found at i:3754722 original size:20 final size:19
Alignment explanation
Indices: 3754697--3754753 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
3754687 ACATTGCAGC
3754697 CAGGGTGTATGGATACACT
1 CAGGGTGTATGGATACACT
* *
3754716 GCAGGGTATATCGATACACT
1 -CAGGGTGTATGGATACACT
3754736 -A--GTGTATGGATACACT
1 CAGGGTGTATGGATACACT
3754752 CA
1 CA
3754754 TAGCTGTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 13 0.41
17 1 0.03
18 1 0.03
20 17 0.53
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (19 bp):
CAGGGTGTATGGATACACT
Found at i:3754764 original size:36 final size:36
Alignment explanation
Indices: 3754701--3754772 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
3754691 TGCAGCCAGG
* *
3754701 GTGTATGGATACACTGCAGGGTATATCGATACACTA
1 GTGTATGGATACACTGCAAGCTATATCGATACACTA
* *
3754737 GTGTATGGATACACT-CATAGCTGTATCGGTACACTA
1 GTGTATGGATACACTGCA-AGCTATATCGATACACTA
3754773 TTTGCATTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 2 0.06
36 29 0.94
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (36 bp):
GTGTATGGATACACTGCAAGCTATATCGATACACTA
Found at i:3758689 original size:19 final size:18
Alignment explanation
Indices: 3758652--3758700 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
3758642 CCATGTTGAT
3758652 AAATAATTTAAAAATAAA
1 AAATAATTTAAAAATAAA
* *
3758670 AAATACTTTCAAAATAAA
1 AAATAATTTAAAAATAAA
*
3758688 AAA-AATTCAAAAA
1 AAATAATTTAAAAA
3758701 GTATTAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATAATTTAAAAATAAA
Found at i:3759238 original size:11 final size:11
Alignment explanation
Indices: 3759222--3759246 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3759212 TTAAAAATAT
3759222 TTGGTTTATAG
1 TTGGTTTATAG
3759233 TTGGTTTATAG
1 TTGGTTTATAG
3759244 TTG
1 TTG
3759247 AAAACATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (11 bp):
TTGGTTTATAG
Found at i:3763866 original size:21 final size:21
Alignment explanation
Indices: 3763842--3763882 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3763832 GAGTATGTAG
3763842 CTTTAAGAGTGTATCTGTGAA
1 CTTTAAGAGTGTATCTGTGAA
* *
3763863 CTTTACGAGTGTATGTGTGA
1 CTTTAAGAGTGTATCTGTGA
3763883 GGTTGTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (21 bp):
CTTTAAGAGTGTATCTGTGAA
Found at i:3766933 original size:21 final size:21
Alignment explanation
Indices: 3766909--3766948 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3766899 AAATATTATT
* *
3766909 TAAAATATTATTATTTTTACC
1 TAAAACATTAATATTTTTACC
3766930 TAAAACATTAATATTTTTA
1 TAAAACATTAATATTTTTA
3766949 ATATTTCTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAAACATTAATATTTTTACC
Found at i:3767375 original size:21 final size:21
Alignment explanation
Indices: 3767345--3767551 Score: 205
Period size: 21 Copynumber: 10.0 Consensus size: 21
3767335 GATTTACATA
*
3767345 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
3767366 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
3767387 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
3767408 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
3767429 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* *
3767452 TT--CGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
3767473 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
3767492 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
3767511 TTCGTGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
3767534 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
3767552 AATCGCAACG
Statistics
Matches: 167, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
19 34 0.20
21 116 0.69
23 17 0.10
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:3767420 original size:63 final size:62
Alignment explanation
Indices: 3767351--3767551 Score: 241
Period size: 63 Copynumber: 3.2 Consensus size: 62
3767341 CATATTCGCA
* *
3767351 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGA-TAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAGTT--CG
* * * * *
3767414 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCGAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
*
3767477 TTGCGATAGTCCAAGTT--CGTTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
3767538 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
3767552 AATCGCAACG
Statistics
Matches: 119, Mismatches: 13, Indels: 14
0.82 0.09 0.10
Matches are distributed among these distances:
59 8 0.07
61 43 0.36
63 52 0.44
65 16 0.13
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (62 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAGTTCG
Found at i:3767525 original size:82 final size:83
Alignment explanation
Indices: 3767391--3767544 Score: 265
Period size: 82 Copynumber: 1.9 Consensus size: 83
3767381 TCGAAGTTCG
*
3767391 CGTTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 CGTTGCGATAGTCCAAGTTC-CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
3767456 TTGCGATTTATTCCAAATT
65 TTGCGATTTATTCCAAATT
* *
3767475 CGTTGCGATAGTCCAAGTT-CGTTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAGTTCGT
1 CGTTGCGATAGTCCAAGTTCCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
3767539 TGCGAT
66 TGCGAT
3767545 AGTCCAAAAT
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
82 49 0.73
84 18 0.27
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (83 bp):
CGTTGCGATAGTCCAAGTTCCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
TGCGATTTATTCCAAATT
Found at i:3768283 original size:23 final size:21
Alignment explanation
Indices: 3768252--3768314 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
3768242 ACTATTGCAA
*
3768252 CGAATTTGGAATAAATCGCAACG
1 CGAACTTGGAAT--ATCGCAACG
*
3768275 CGAACTTGGACTATCGCAACG
1 CGAACTTGGAATATCGCAACG
* *
3768296 CAAACTTGGACTATCGCAA
1 CGAACTTGGAATATCGCAA
3768315 TGTGAATATG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 27 0.73
23 10 0.27
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (21 bp):
CGAACTTGGAATATCGCAACG
Found at i:3768290 original size:21 final size:21
Alignment explanation
Indices: 3768266--3768314 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
3768256 TTTGGAATAA
*
3768266 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCAAACTTGGACT
3768287 ATCGCAACGCAAACTTGGACT
1 ATCGCAACGCAAACTTGGACT
3768308 ATCGCAA
1 ATCGCAA
3768315 TGTGAATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCAAACTTGGACT
Found at i:3768401 original size:21 final size:21
Alignment explanation
Indices: 3768377--3768425 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3768367 AATTTGGAAA
*
3768377 ATCGTAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
3768398 ATCGCAATGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
3768419 ATCGCAA
1 ATCGCAA
3768426 TAATAATATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:3768414 original size:111 final size:113
Alignment explanation
Indices: 3768252--3768471 Score: 356
Period size: 111 Copynumber: 2.0 Consensus size: 113
3768242 ACTATTGCAA
*
3768252 CGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGCAAACTTGGACTATCGCAAT-
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGCAAACTTGGACTATCGCAATA
* *
3768316 GTGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGT
66 AT-AATATGTAAATCGCAATACGATAGTCGAAGTTCGCGTTGCGATAGT
* * *
3768365 CGAATTTGG-A-AAATCGTAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGCAAACTTGGACTATCGCAATA
3768428 ATAATATGTAAATCGCAATACGATAGTCGAAGTTCGCGTTGCGA
66 ATAATATGTAAATCGCAATACGATAGTCGAAGTTCGCGTTGCGA
3768472 ATCTGGAAAC
Statistics
Matches: 100, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
111 89 0.89
112 2 0.02
113 9 0.09
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (113 bp):
CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGCAAACTTGGACTATCGCAATA
ATAATATGTAAATCGCAATACGATAGTCGAAGTTCGCGTTGCGATAGT
Found at i:3768426 original size:21 final size:21
Alignment explanation
Indices: 3768385--3768426 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3768375 AAATCGTAAC
3768385 GCGAACTTCGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
*
3768406 GCGAACTTGGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
3768427 AATAATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
GCGAACTTCGACTATCGCAAT
Found at i:3771913 original size:15 final size:15
Alignment explanation
Indices: 3771895--3771927 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3771885 ATCAACAGAT
3771895 ATAATTTTTATATAA
1 ATAATTTTTATATAA
*
3771910 ATAATTTTTATTTAA
1 ATAATTTTTATATAA
3771925 ATA
1 ATA
3771928 CTCAAGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATTTTTATATAA
Found at i:3771934 original size:58 final size:58
Alignment explanation
Indices: 3771860--3771985 Score: 243
Period size: 58 Copynumber: 2.2 Consensus size: 58
3771850 ATACATGATA
3771860 TATTTAAATACTCAAGTAATATATTATCAACAGATATAATTTTTATATAAATAATTTT
1 TATTTAAATACTCAAGTAATATATTATCAACAGATATAATTTTTATATAAATAATTTT
*
3771918 TATTTAAATACTCAAGTAATATATTATCAACATATATAATTTTTATATAAATAATTTT
1 TATTTAAATACTCAAGTAATATATTATCAACAGATATAATTTTTATATAAATAATTTT
3771976 TATTTAAATA
1 TATTTAAATA
3771986 TTTAGAATTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
58 67 1.00
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (58 bp):
TATTTAAATACTCAAGTAATATATTATCAACAGATATAATTTTTATATAAATAATTTT
Found at i:3771971 original size:15 final size:15
Alignment explanation
Indices: 3771953--3771985 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3771943 ATCAACATAT
3771953 ATAATTTTTATATAA
1 ATAATTTTTATATAA
*
3771968 ATAATTTTTATTTAA
1 ATAATTTTTATATAA
3771983 ATA
1 ATA
3771986 TTTAGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATTTTTATATAA
Found at i:3772177 original size:20 final size:20
Alignment explanation
Indices: 3772141--3772178 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3772131 ATCCTATTCC
*
3772141 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTCATTCCCA
3772161 CTGGTAAT-TTTACATTCC
1 CTGGTAATCTTT-CATTCC
3772179 GTAAACCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTTCATTCCCA
Found at i:3774120 original size:17 final size:17
Alignment explanation
Indices: 3774098--3774150 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
3774088 AATTAAGAGT
3774098 TAGTTTAATATATGAAC
1 TAGTTTAATATATGAAC
*
3774115 TAGTTTGATGA-ATGAAC
1 TAGTTTAAT-ATATGAAC
3774132 TAGTTTAAT-TAATGAAC
1 TAGTTTAATAT-ATGAAC
3774149 TA
1 TA
3774151 ACTTTATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 30 0.97
18 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (17 bp):
TAGTTTAATATATGAAC
Found at i:3774161 original size:18 final size:18
Alignment explanation
Indices: 3774125--3774168 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3774115 TAGTTTGATG
*
3774125 AATGAACT-AGTTTAATT
1 AATGAACTAACTTTAATT
*
3774142 AATGAACTAACTTTATTT
1 AATGAACTAACTTTAATT
3774160 AATGAACTA
1 AATGAACTA
3774169 GATGCATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (18 bp):
AATGAACTAACTTTAATT
Found at i:3775496 original size:32 final size:31
Alignment explanation
Indices: 3775446--3775535 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 31
3775436 TAATAAAATA
* **
3775446 TTTAAATAATGATGATTAAATATATTATTAT
1 TTTAAATAATAAAAATTAAATATATTATTAT
* * *
3775477 TTTAATTAATATCAAATTAAATA-A--AGTA-
1 TTTAAATAATA-AAAATTAAATATATTATTAT
*
3775505 TTTAAATAATAAAAATCAAATATATTATTAT
1 TTTAAATAATAAAAATTAAATATATTATTAT
3775536 ATAAAATTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 10
0.69 0.16 0.16
Matches are distributed among these distances:
27 9 0.20
28 11 0.25
29 3 0.07
30 3 0.07
31 10 0.23
32 8 0.18
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.43
Consensus pattern (31 bp):
TTTAAATAATAAAAATTAAATATATTATTAT
Found at i:3775533 original size:27 final size:28
Alignment explanation
Indices: 3775471--3775533 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 28
3775461 TTAAATATAT
* * *
3775471 TATTATTTTAATTAATATCAAATTAAATA
1 TATTA-TTTAAATAATATAAAATCAAATA
* *
3775500 AAGTATTTAAATAATA-AAAATCAAATA
1 TATTATTTAAATAATATAAAATCAAATA
3775527 TATTATT
1 TATTATT
3775534 ATATAAAATT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
27 14 0.52
28 10 0.37
29 3 0.11
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (28 bp):
TATTATTTAAATAATATAAAATCAAATA
Found at i:3775660 original size:47 final size:47
Alignment explanation
Indices: 3775563--3775659 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 47
3775553 CCACGTCAAC
* * *
3775563 AAATAATTTCAGAGTTAACTGTGATAACTTGACTGGAATCAAATAAA
1 AAATAATTTAAGAGTTAACCGTGATAACTTGACTAGAATCAAATAAA
*
3775610 AAATAATTTAAGAGTTAACCGTGGATAACTTGACTAGAATCAAATGAA
1 AAATAATTTAAGAGTTAACCGT-GATAACTTGACTAGAATCAAATAAA
3775658 AA
1 AA
3775660 TTTTGATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 20 0.44
48 25 0.56
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (47 bp):
AAATAATTTAAGAGTTAACCGTGATAACTTGACTAGAATCAAATAAA
Found at i:3776474 original size:3 final size:3
Alignment explanation
Indices: 3776466--3776491 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3776456 TTTTAAAATA
3776466 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
3776492 AGATTCAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:3793901 original size:2 final size:2
Alignment explanation
Indices: 3793894--3793920 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3793884 TTTCTATTTA
3793894 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3793921 ATTTAAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3799161 original size:20 final size:19
Alignment explanation
Indices: 3799132--3799176 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3799122 GTTTAATTTT
*
3799132 ATTA-AATTTATTGAATTAA
1 ATTAGAATTTA-TGAATAAA
*
3799151 ATTAGAATTTATGAGTAAA
1 ATTAGAATTTATGAATAAA
3799170 ATTAGAA
1 ATTAGAA
3799177 GTGTAAGGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (19 bp):
ATTAGAATTTATGAATAAA
Found at i:3820541 original size:24 final size:25
Alignment explanation
Indices: 3820514--3820561 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 25
3820504 TATATGTGAT
3820514 TCATATT-AGTTTA-TATTTTTAATA
1 TCATATTCA-TTTATTATTTTTAATA
3820538 TCATATTCATTTATTTATTTTTAA
1 TCATATTCATTTA-TTATTTTTAA
3820562 GGTGCTTGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 1 0.05
26 9 0.43
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.60
Consensus pattern (25 bp):
TCATATTCATTTATTATTTTTAATA
Found at i:3822697 original size:25 final size:25
Alignment explanation
Indices: 3822668--3822717 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3822658 AAAATGACAC
*
3822668 ATGTCACGTATACATCAATGATGAT
1 ATGTCACATATACATCAATGATGAT
* *
3822693 ATGTCACATGTACATGAATGATGAT
1 ATGTCACATATACATCAATGATGAT
3822718 GTGGTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (25 bp):
ATGTCACATATACATCAATGATGAT
Found at i:3824459 original size:17 final size:18
Alignment explanation
Indices: 3824439--3824472 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3824429 TTTATAAGGT
3824439 ATATTTTGTTA-TATTTA
1 ATATTTTGTTAGTATTTA
3824456 ATATTTTGTTAGTATTT
1 ATATTTTGTTAGTATTT
3824473 TATTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (18 bp):
ATATTTTGTTAGTATTTA
Found at i:3824491 original size:16 final size:15
Alignment explanation
Indices: 3824472--3824513 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
3824462 TGTTAGTATT
3824472 TTATTTAATTATTGTA
1 TTATTTAATT-TTGTA
*
3824488 TTATTTAATTTTTTA
1 TTATTTAATTTTGTA
*
3824503 TTATTTTATTT
1 TTATTTAATTT
3824514 AAATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTATTTAATTTTGTA
Found at i:3824503 original size:20 final size:21
Alignment explanation
Indices: 3824480--3824525 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
3824470 TTTTATTTAA
* *
3824480 TTATTGTATTATTT-AATTTT
1 TTATTATATTATTTAAATATT
*
3824500 TTATTATTTTATTTAAATATT
1 TTATTATATTATTTAAATATT
3824521 TTATT
1 TTATT
3824526 TTTTTGCAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TTATTATATTATTTAAATATT
Found at i:3824509 original size:8 final size:8
Alignment explanation
Indices: 3824440--3824512 Score: 51
Period size: 8 Copynumber: 9.1 Consensus size: 8
3824430 TTATAAGGTA
*
3824440 TATTTTGT
1 TATTTTAT
*
3824448 TATATTTAA
1 TAT-TTTAT
*
3824457 TATTTTGT
1 TATTTTAT
*
3824465 TAGTATT-T
1 TA-TTTTAT
*
3824473 TATTTAAT
1 TATTTTAT
*
3824481 TATTGTAT
1 TATTTTAT
*
3824489 TATTTAAT
1 TATTTTAT
3824497 T-TTTTAT
1 TATTTTAT
3824504 TATTTTAT
1 TATTTTAT
3824512 T
1 T
3824513 TAAATATTTT
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
7 8 0.16
8 32 0.65
9 9 0.18
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (8 bp):
TATTTTAT
Found at i:3824530 original size:21 final size:20
Alignment explanation
Indices: 3824488--3824529 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3824478 AATTATTGTA
*
3824488 TTATTTAATTTTTTATTATT
1 TTATTTAATATTTTATTATT
3824508 TTATTTAAATATTTTATT-TT
1 TTATTT-AATATTTTATTATT
3824528 TT
1 TT
3824530 TGCAGTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTATTTAATATTTTATTATT
Found at i:3827691 original size:2 final size:2
Alignment explanation
Indices: 3827679--3827725 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
3827669 TGTGAACAAG
3827679 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3827722 AT AT
1 AT AT
3827726 GTTTATGTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3828035 original size:32 final size:32
Alignment explanation
Indices: 3827993--3828054 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
3827983 AGTCGAGATT
3827993 TTATCAATGTCTTTCGGGACATATGGACAAAA
1 TTATCAATGTCTTTCGGGACATATGGACAAAA
*
3828025 TTATCTATGTCTTTCGGGACATATGGACAA
1 TTATCAATGTCTTTCGGGACATATGGACAA
3828055 TATACCTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (32 bp):
TTATCAATGTCTTTCGGGACATATGGACAAAA
Found at i:3828117 original size:31 final size:31
Alignment explanation
Indices: 3828002--3828118 Score: 92
Period size: 31 Copynumber: 3.7 Consensus size: 31
3827992 TTTATCAATG
** * *
3828002 TCTTTCGGGACATATGGACAAAATTATCTATG-
1 TCTTT-GGGACATATGGAC-AGTTTACCTAGGT
* * *
3828034 TCTTTCGGGACATATGGACAATATACCTATGT
1 TCTTT-GGGACATATGGACAGTTTACCTAGGT
** * *
3828066 TCTAAGGAACATATGAACAGTTTACCTAGGT
1 TCTTTGGGACATATGGACAGTTTACCTAGGT
*
3828097 TCTTTGGGACCTATGGACAGTT
1 TCTTTGGGACATATGGACAGTT
3828119 GTCGAGGTTT
Statistics
Matches: 69, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
31 47 0.68
32 22 0.32
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (31 bp):
TCTTTGGGACATATGGACAGTTTACCTAGGT
Found at i:3828971 original size:21 final size:21
Alignment explanation
Indices: 3828945--3828985 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3828935 TATGGGCAAA
3828945 GTGTATCGATGCACATTCAAT
1 GTGTATCGATGCACATTCAAT
* *
3828966 GTGTATCGATGGACTTTCAA
1 GTGTATCGATGCACATTCAA
3828986 ATAAATGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (21 bp):
GTGTATCGATGCACATTCAAT
Found at i:3830674 original size:23 final size:23
Alignment explanation
Indices: 3830648--3830699 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
3830638 ATGGCATTTT
*
3830648 GGTGCAATTCTACGCGGCACTTC
1 GGTGCAATTCTACGCGACACTTC
*
3830671 GGTGCAATTCTACGTGACACTTC
1 GGTGCAATTCTACGCGACACTTC
3830694 GGTGCA
1 GGTGCA
3830700 TTTATACGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGTGCAATTCTACGCGACACTTC
Found at i:3835386 original size:12 final size:12
Alignment explanation
Indices: 3835367--3835411 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
3835357 AATACTTTTA
3835367 AAAT-TTAAAAT
1 AAATATTAAAAT
3835378 AAATATTAAAAT
1 AAATATTAAAAT
* *
3835390 AATTATTCAAAT
1 AAATATTAAAAT
3835402 AAATA-TAAAA
1 AAATATTAAAA
3835412 GAGTAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 8 0.28
12 21 0.72
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATATTAAAAT
Found at i:3839629 original size:2 final size:2
Alignment explanation
Indices: 3839622--3839660 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3839612 CGTGGGACAA
3839622 CT CT CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3839661 GGCACTTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3841122 original size:22 final size:22
Alignment explanation
Indices: 3841095--3841141 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
3841085 TTCAATTTTG
*
3841095 TTTAAA-AAAATTATATAAATTT
1 TTTAAAGAAAA-TATATAAATAT
3841117 TTTAAAGAAAATATATAAATAT
1 TTTAAAGAAAATATATAAATAT
3841139 TTT
1 TTT
3841142 CCAACTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TTTAAAGAAAATATATAAATAT
Found at i:3841306 original size:644 final size:651
Alignment explanation
Indices: 3840047--3841345 Score: 2004
Period size: 644 Copynumber: 2.0 Consensus size: 651
3840037 GTTTCTCTAA
*
3840047 GGTGTGTTTGGGTGAGGGAATGTGAGATTCTCATGGGAATGAAATCCACATTCCTCCGTTTGGTT
1 GGTGTGTTTGGGTGAGGGAATGTGAGATTCTCATGGGAATGAAATCCACATTCCCCCGTTTGGTT
* * *
3840112 GGCCAGGAATGTCATTCCCGGTAATCTTACATTATCAATAGTGGATTTTTAGGGGTATATTACCG
66 GGCCAGGAATGTCATTCCCGGTAATCTTACATTAGCAATAGTAGATTTTTAGGGGTATAATACCG
* * *
3840177 GGAATCTCATTACCTCTATTTCCTTAGGTATTGTTGGATTACCGGTGTTTTGGACTAAAATGCCC
131 AGAATCTCATTACCTCTATTTCCTTAGGTATTGTTGGATTACCAGCGTTTTGGACTAAAATGCCC
* * * *
3840242 TTAAAAAAATTTCTTTCAAAAATATTTTTATTTTGTCATTGAATAATAAAAATTCTATGAAAATT
196 TT--AAAAATTTCTTTCAAAAATATCTTTATTCTATCATTGAATAATAAAAATTCTACGAAAATT
3840307 AAATTACAAATTTATCCTTAAACTATTTTAGATTTACAAAAAAAAAATCTATAATTAAAATTTTA
259 AAATTACAAATTTATCCTTAAACTATTTTAGATTTACAAAAAAAAAATCTATAATTAAAATTTTA
*
3840372 TATAAAGTTCAGGGGTTAAAATAAAATTTTACCATTTCATTAAACATTTTTATATTTTTAATTTT
324 TATAAAGTTCAGGGGTTAAAATAAAATTTTACCATTTCATTAAACATTTTTATATTTTCAATTTT
3840437 GTAAAAAAAATTATATAAATTTTATGAATTTAAATTTTTAAAGAAAATATATAAATATTTTCCAA
389 GTAAAAAAAATTATAT-AA--TTA-GAA-TT--ATTTTTAAAGAAAATATATAAATATTTTCCAA
*
3840502 CTTGTTAAAAAATAAATATATAATAAGGATAATTTGGTCAAATATACATTCCAATAATCTTTTAT
447 CTTGTTAAAAAATAAATATATAATAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTAT
* * *
3840567 TCCTTTAACCAAACACGGTAATCTTACATTCCTGCTAAATCAACCAAACACAAAATACAACATTC
512 TCCTCTAACCAAACACGATAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTC
* * * ** **
3840632 CCATTAATCATATTCCCTGGTAATCTTTTATTCCCACTGGTAATCTTACATTTTGTGAACCAAAC
577 ACAATAATCATATTCCATAATAATCTTTTATTCCCACTGGTAATCTTACATTCCGTGAACCAAAC
3840697 GCACCATAAG
642 GCACCATAAG
* * * *
3840707 GGTGTGTTTGGTTGGGGGAATGTGAGATTCTCATGGGAATGGAATCTACATTCCCCCGTTTGGTT
1 GGTGTGTTTGGGTGAGGGAATGTGAGATTCTCATGGGAATGAAATCCACATTCCCCCGTTTGGTT
* *
3840772 GGCCGGGAATGTCATTCCCGGTAATCTTACATTAGCAATAGTAGATTTTTTGGGGTATAATACCG
66 GGCCAGGAATGTCATTCCCGGTAATCTTACATTAGCAATAGTAGATTTTTAGGGGTATAATACCG
* *
3840837 AGAATGTCATTACCTCTCTTTCCTTAGGTATTGTTGGATTACCAGCGTTTTGGACTAAAATGCCC
131 AGAATCTCATTACCTCTATTTCCTTAGGTATTGTTGGATTACCAGCGTTTTGGACTAAAATGCCC
** * * *
3840902 TT-AATTTTTTTTTCCAAAAATATCTTTATTCTATCATTGAATAATAAAAATTTTACGAAAGTTA
196 TTAAAAATTTCTTT-CAAAAATATCTTTATTCTATCATTGAATAATAAAAATTCTACGAAAATTA
* *
3840966 AATTATAAATTTATCCTTAAACTATTTTAGATTTAC-AAAAAAAAGTCTATAATTAAAATTTTAT
260 AATTACAAATTTATCCTTAAACTATTTTAGATTTACAAAAAAAAAATCTATAATTAAAATTTTAT
* * * *
3841030 ATGAAGTTCAGGGGTTAAAATAAAATTTTACCCTTTCTTTAAACCTTTTTATATTTTCAATTTTG
325 ATAAAGTTCAGGGGTTAAAATAAAATTTTACCATTTCATTAAACATTTTTATATTTTCAATTTTG
*
3841095 TTTAAAAAAA-T-TAT-A-TA-AA-T-TTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTA
390 -TAAAAAAAATTATATAATTAGAATTATTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTA
*
3841153 AAAAATAAATATATAATAAGGACACTTTGGTCAAATATACATTCCAATAATCTTTTATTCCTCTA
454 AAAAATAAATATATAATAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTCTA
* *
3841218 ACCAAACACGATAATCTTACATTCCTGTTAAACCAACCAAACACAAAATACAATATTCACAATAA
519 ACCAAACACGATAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCACAATAA
* *
3841283 TCATATTCCATAATAATCTTTTATTCCCACTTGTAATCTTATATTCCGTGAACCAAACGCACC
584 TCATATTCCATAATAATCTTTTATTCCCACTGGTAATCTTACATTCCGTGAACCAAACGCACC
3841346 TTAAAGGATT
Statistics
Matches: 589, Mismatches: 48, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
644 215 0.37
647 1 0.00
649 2 0.00
651 2 0.00
654 1 0.00
656 3 0.01
657 96 0.16
658 87 0.15
660 182 0.31
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (651 bp):
GGTGTGTTTGGGTGAGGGAATGTGAGATTCTCATGGGAATGAAATCCACATTCCCCCGTTTGGTT
GGCCAGGAATGTCATTCCCGGTAATCTTACATTAGCAATAGTAGATTTTTAGGGGTATAATACCG
AGAATCTCATTACCTCTATTTCCTTAGGTATTGTTGGATTACCAGCGTTTTGGACTAAAATGCCC
TTAAAAATTTCTTTCAAAAATATCTTTATTCTATCATTGAATAATAAAAATTCTACGAAAATTAA
ATTACAAATTTATCCTTAAACTATTTTAGATTTACAAAAAAAAAATCTATAATTAAAATTTTATA
TAAAGTTCAGGGGTTAAAATAAAATTTTACCATTTCATTAAACATTTTTATATTTTCAATTTTGT
AAAAAAAATTATATAATTAGAATTATTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAAA
AAATAAATATATAATAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTCTAAC
CAAACACGATAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCACAATAATC
ATATTCCATAATAATCTTTTATTCCCACTGGTAATCTTACATTCCGTGAACCAAACGCACCATAA
G
Found at i:3846137 original size:4 final size:4
Alignment explanation
Indices: 3846120--3846183 Score: 92
Period size: 4 Copynumber: 16.0 Consensus size: 4
3846110 AAGTCTTTAA
* *
3846120 ATAT ACAT ACAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* *
3846168 ATAT ATTT ATTT ATAT
1 ATAT ATAT ATAT ATAT
3846184 CTTTCAATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:3846143 original size:10 final size:10
Alignment explanation
Indices: 3846120--3846183 Score: 92
Period size: 10 Copynumber: 6.4 Consensus size: 10
3846110 AAGTCTTTAA
* *
3846120 ATATACATAC
1 ATATATATAT
3846130 ATATATATAT
1 ATATATATAT
3846140 ATATATATAT
1 ATATATATAT
3846150 ATATATATAT
1 ATATATATAT
3846160 ATATATATAT
1 ATATATATAT
* *
3846170 ATATTTATTT
1 ATATATATAT
3846180 ATAT
1 ATAT
3846184 CTTTCAATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 50 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (10 bp):
ATATATATAT
Found at i:3846799 original size:25 final size:25
Alignment explanation
Indices: 3846765--3846815 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
3846755 GTTGGGCCAT
**
3846765 TCTGAATATTTAGTTATTCTCGAAA
1 TCTGAATATTTAGTTAACCTCGAAA
3846790 TCTGAATATTTAGTTAACCTCGAAA
1 TCTGAATATTTAGTTAACCTCGAAA
3846815 T
1 T
3846816 TACTGACCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (25 bp):
TCTGAATATTTAGTTAACCTCGAAA
Found at i:3854528 original size:2 final size:2
Alignment explanation
Indices: 3854521--3854563 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3854511 ACCATATAAA
3854521 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3854563 A
1 A
3854564 CGGTTAAGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3862679 original size:2 final size:2
Alignment explanation
Indices: 3862672--3862696 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3862662 GAGAATGGTT
3862672 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3862697 TTGAGAACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3864681 original size:21 final size:22
Alignment explanation
Indices: 3864645--3864686 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
3864635 ATTTTTTGAT
3864645 TAATTTATATTTAAATATAAAC
1 TAATTTATATTTAAATATAAAC
*
3864667 TAATTTATA-TTAAATCTAAA
1 TAATTTATATTTAAATATAAA
3864687 ATCTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATTTATATTTAAATATAAAC
Found at i:3865756 original size:136 final size:136
Alignment explanation
Indices: 3865581--3865830 Score: 369
Period size: 136 Copynumber: 1.8 Consensus size: 136
3865571 TTTGAAATCA
* *
3865581 ATTTTTAGCTATAATGATAAGAATTTTATCATAAATTATCATTTTATCTTATGTTATTCTTTT-G
1 ATTTATAGCTATAATGATAAGAATTTTATCATAAATTATCATTTTATCCTATGTTATT-TTTTGG
*
3865645 AGTATTTTATTCCATAATATTTCAATTTTGGTCAAAATAAACTTTATTAGCCGTTAATTGATTAA
65 AGTATTTTATTCCACAATATTTCAATTTTGGTCAAAATAAACTTTATTAGCCGTTAATTGATTAA
3865710 TGATGAG
130 TGATGAG
* * * *
3865717 ATTTATAGCTATAAT-AGTAATATTTTTATTATAAATTATCTTTTTATCCTATGTTATTTTTTGG
1 ATTTATAGCTATAATGA-TAAGAATTTTATCATAAATTATCATTTTATCCTATGTTATTTTTTGG
** * *
3865781 AGTATTTTATTTTACAATGTTTTAATTTTGGTCAAAATAAACTTTATTAG
65 AGTATTTTATTCCACAATATTTCAATTTTGGTCAAAATAAACTTTATTAG
3865831 TTGAAAACTA
Statistics
Matches: 101, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
135 5 0.05
136 96 0.95
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (136 bp):
ATTTATAGCTATAATGATAAGAATTTTATCATAAATTATCATTTTATCCTATGTTATTTTTTGGA
GTATTTTATTCCACAATATTTCAATTTTGGTCAAAATAAACTTTATTAGCCGTTAATTGATTAAT
GATGAG
Found at i:3877218 original size:26 final size:26
Alignment explanation
Indices: 3877171--3877242 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
3877161 ACAAAACTAA
*
3877171 TCAAAATTTATATAAGCA-TTTTTTG
1 TCAAAAATTATATAAGCATTTTTTTG
3877196 TCAAAAATTATATAAGCATTTTTTTG
1 TCAAAAATTATATAAGCATTTTTTTG
*
3877222 TCAAAAAATATATAAGCATTT
1 TCAAAAATTATATAAGCATTT
3877243 AATTTTTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
25 17 0.39
26 27 0.61
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (26 bp):
TCAAAAATTATATAAGCATTTTTTTG
Found at i:3880163 original size:2 final size:2
Alignment explanation
Indices: 3880156--3880219 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
3880146 AGGTAAGAGA
3880156 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3880198 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
3880220 CGTAAAACTC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3884038 original size:2 final size:2
Alignment explanation
Indices: 3884033--3884060 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3884023 TCTCTCTTCC
3884033 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3884061 CTTTGGCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3884592 original size:11 final size:12
Alignment explanation
Indices: 3884566--3884594 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3884556 ACATCAATTT
3884566 AGTTAGGTGAAG
1 AGTTAGGTGAAG
3884578 AGTTAGGTG-AG
1 AGTTAGGTGAAG
3884589 AGTTAG
1 AGTTAG
3884595 TTATTTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (12 bp):
AGTTAGGTGAAG
Found at i:3888064 original size:20 final size:20
Alignment explanation
Indices: 3888039--3888076 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3888029 CACATGTTAA
3888039 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
3888059 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
3888077 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:3890805 original size:12 final size:12
Alignment explanation
Indices: 3890788--3890842 Score: 94
Period size: 12 Copynumber: 4.7 Consensus size: 12
3890778 ACATCAATTT
3890788 AGTTAGGTGAAG
1 AGTTAGGTGAAG
3890800 AGTTAGGTGAAG
1 AGTTAGGTGAAG
*
3890812 AATTAGGTGAAG
1 AGTTAGGTGAAG
3890824 AGTTAGGTG-AG
1 AGTTAGGTGAAG
3890835 AGTTAGGT
1 AGTTAGGT
3890843 ATTTGTATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
11 10 0.24
12 31 0.76
ACGTcount: A:0.33, C:0.00, G:0.40, T:0.27
Consensus pattern (12 bp):
AGTTAGGTGAAG
Found at i:3892363 original size:74 final size:72
Alignment explanation
Indices: 3892242--3892389 Score: 224
Period size: 72 Copynumber: 2.0 Consensus size: 72
3892232 TATATATAGT
*
3892242 TCATTTCTAATCAACCATAAACTAATACCAAAAAGAAAAATATATATATAACTAACTCTTTAATA
1 TCATTTCTAATCAACCATAAACTAATACCAAAAAG--AAATATATATATAACTAACTCCTTAATA
3892307 AACTAACAA
64 AACTAACAA
* * * * *
3892316 TCATTTCTAATTAACCATAAAGTAATACCAAATAGAAATATATATATAATTAATTCCTTAATAAA
1 TCATTTCTAATCAACCATAAACTAATACCAAAAAGAAATATATATATAACTAACTCCTTAATAAA
3892381 CTAACAA
66 CTAACAA
3892388 TC
1 TC
3892390 TTAATCAGGG
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
72 36 0.53
74 32 0.47
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.31
Consensus pattern (72 bp):
TCATTTCTAATCAACCATAAACTAATACCAAAAAGAAATATATATATAACTAACTCCTTAATAAA
CTAACAA
Found at i:3896714 original size:26 final size:26
Alignment explanation
Indices: 3896685--3896765 Score: 71
Period size: 27 Copynumber: 3.2 Consensus size: 26
3896675 TATAATATTT
3896685 TAAA-ATTAATAATTATTTTTTTATAA
1 TAAATATTAATAATTATTTTTTTA-AA
* * * *
3896711 TAAATAATATTAATTATTATATTAAA
1 TAAATATTAATAATTATTTTTTTAAA
3896737 TAAATATCATAA-AA-TA-TTTTTTAAA
1 TAAATAT--TAATAATTATTTTTTTAAA
3896762 TAAA
1 TAAA
3896766 ATTTTTAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
25 11 0.25
26 14 0.32
27 17 0.39
28 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (26 bp):
TAAATATTAATAATTATTTTTTTAAA
Found at i:3900349 original size:127 final size:125
Alignment explanation
Indices: 3900123--3900619 Score: 598
Period size: 127 Copynumber: 3.8 Consensus size: 125
3900113 GGCAAAGTGG
3900123 TGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
3900188 TTATGTCACTCATGTCCCCCGGAGAACTATTCATGTCAATACCTATTATTTCTGAGGAGACT
66 TTATGTCACTCATGTCCCCC-GAGAACTATTCATGTCAATACCTATTATTTCTGAGG-GACT
* *
3900250 TGAAAGCGCGTTCCCGGGGGTGCGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
3900315 TTATGTCACTCATGTCCCCCAATGAACTATTCATGTCAGTACCTATTATTTCTGAGCGGACT
66 TTATGTCACTCATGTCCCCCGA-GAACTATTCATGTCAATACCTATTATTTCTGAG-GGACT
* * *
3900377 TGAAAGCGCGTTCTCGGGGGCGCGCCTTCTATTATTTTGTTAGAGAATATGTTATCATTGCCCTA
1 TGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * *
3900442 TAATGTTACTCATGTCCCCCGGGGAACTATTCATGTCACCCGGGGAACTATTCATGTCAGTACCT
66 TTATGTCACTCATGTCCCCC-GAGAACTATTCA--T--------G------TCA----A-TACCT
* *
3900507 ATTATTTCTAAAGGGACT
109 ATTATTTCTGAGG-GACT
* * *
3900525 TGAAAGCGCGTTCCCGAGGGCGCTCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGTCCTA
1 TGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
3900590 TTATGTCACTCATGTCCCCCGGGGAACTAT
66 TTATGTCACTCATGTCCCCC-GAGAACTAT
3900620 AGATGAATGG
Statistics
Matches: 321, Mismatches: 24, Indels: 29
0.86 0.06 0.08
Matches are distributed among these distances:
126 1 0.00
127 207 0.64
128 1 0.00
129 1 0.00
137 1 0.00
143 3 0.01
147 1 0.00
148 106 0.33
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (125 bp):
TGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTTCTGAGGGACT
Found at i:3900477 original size:21 final size:21
Alignment explanation
Indices: 3900451--3900500 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
3900441 ATAATGTTAC
*
3900451 TCATGTCCCCCGGGGAACTAT
1 TCATGTCACCCGGGGAACTAT
3900472 TCATGTCACCCGGGGAACTAT
1 TCATGTCACCCGGGGAACTAT
3900493 TCATGTCA
1 TCATGTCA
3900501 GTACCTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (21 bp):
TCATGTCACCCGGGGAACTAT
Found at i:3900601 original size:148 final size:148
Alignment explanation
Indices: 3900338--3900619 Score: 467
Period size: 148 Copynumber: 1.9 Consensus size: 148
3900328 GTCCCCCAAT
* * *
3900338 GAACTATTCATGTCAGTACCTATTATTTCTGAGCGGACTTGAAAGCGCGTTCTCGGGGGCGCGCC
1 GAACTATTCATGTCAGTACCTATTATTTCTAAGCGGACTTGAAAGCGCGTTCCCGAGGGCGCGCC
* * *
3900403 TTCTATTATTTTGTTAGAGAATATGTTATCATTGCCCTATAATGTTACTCATGTCCCCCGGGGAA
66 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATAATGTCACTCATGTCCCCCGGGGAA
3900468 CTATTCATGTCACCCGGG
131 CTATTCATGTCACCCGGG
*
3900486 GAACTATTCATGTCAGTACCTATTATTTCTAAAG-GGACTTGAAAGCGCGTTCCCGAGGGCGCTC
1 GAACTATTCATGTCAGTACCTATTATTTCT-AAGCGGACTTGAAAGCGCGTTCCCGAGGGCGCGC
* *
3900550 CTTCCATTATTTTGTCAGAGAATATGTTATCATTGTCCTATTATGTCACTCATGTCCCCCGGGGA
65 CTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATAATGTCACTCATGTCCCCCGGGGA
3900615 ACTAT
130 ACTAT
3900620 AGATGAATGG
Statistics
Matches: 124, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
148 122 0.98
149 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (148 bp):
GAACTATTCATGTCAGTACCTATTATTTCTAAGCGGACTTGAAAGCGCGTTCCCGAGGGCGCGCC
TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATAATGTCACTCATGTCCCCCGGGGAA
CTATTCATGTCACCCGGG
Found at i:3900897 original size:14 final size:14
Alignment explanation
Indices: 3900878--3900909 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3900868 GTGTTAAGTT
3900878 TGTTTTAATATATA
1 TGTTTTAATATATA
*
3900892 TGTTTTAATGTATA
1 TGTTTTAATATATA
3900906 TGTT
1 TGTT
3900910 AAGGATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (14 bp):
TGTTTTAATATATA
Found at i:3901056 original size:34 final size:34
Alignment explanation
Indices: 3901017--3901089 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
3901007 TTAAGTTGAA
* *
3901017 TTTAATGTTAAATTTCAAATGCTATAATTTGTAT
1 TTTAATGTTAAATTTCAAATACTATAATATGTAT
* **
3901051 TTTAATTTTAAATTTTGAATACTATAATATGTAT
1 TTTAATGTTAAATTTCAAATACTATAATATGTAT
*
3901085 ATTAA
1 TTTAA
3901090 AAACATTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (34 bp):
TTTAATGTTAAATTTCAAATACTATAATATGTAT
Found at i:3901669 original size:21 final size:22
Alignment explanation
Indices: 3901610--3901671 Score: 101
Period size: 21 Copynumber: 2.9 Consensus size: 22
3901600 AAAACCCTAT
*
3901610 GGGCTAGGCATGTAA-CCTGGC
1 GGGCTAGGAATGTAACCCTGGC
3901631 GGGCTAGGAATGTAACCCTGG-
1 GGGCTAGGAATGTAACCCTGGC
3901652 GGGCTAGGAATGTAACCCTG
1 GGGCTAGGAATGTAACCCTG
3901672 CGGAGATGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 34 0.87
22 5 0.13
ACGTcount: A:0.23, C:0.21, G:0.37, T:0.19
Consensus pattern (22 bp):
GGGCTAGGAATGTAACCCTGGC
Found at i:3901698 original size:42 final size:41
Alignment explanation
Indices: 3901648--3901740 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 41
3901638 GAATGTAACC
* *
3901648 CTGGGGGCTAGGAATGTAACCCTGCGGAGATGACATATAAA
1 CTGGGGGCTAGGAATATAACCCTGAGGAGATGACATATAAA
* * ** * *
3901689 CTGGTGGGCTTGGTATATGCCCCTGAGGAGATGGCATATGAA
1 CTGG-GGGCTAGGAATATAACCCTGAGGAGATGACATATAAA
3901731 CTGGAGGGCT
1 CTGG-GGGCT
3901741 GGGCATCATC
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 4 0.10
42 38 0.90
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23
Consensus pattern (41 bp):
CTGGGGGCTAGGAATATAACCCTGAGGAGATGACATATAAA
Found at i:3903487 original size:15 final size:15
Alignment explanation
Indices: 3903456--3903530 Score: 73
Period size: 15 Copynumber: 5.1 Consensus size: 15
3903446 ATAAATAATT
*
3903456 AATAA-ATTTAAATA
1 AATAATATTTATATA
*
3903470 AATAATAATTATATA
1 AATAATATTTATATA
* * *
3903485 AATATTATTTAAAAA
1 AATAATATTTATATA
3903500 AATAATATTTATAT-
1 AATAATATTTATATA
* *
3903514 AATTATATTAATATA
1 AATAATATTTATATA
3903529 AA
1 AA
3903531 ATATAAAAAC
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
14 17 0.35
15 31 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATAATATTTATATA
Found at i:3904973 original size:6 final size:6
Alignment explanation
Indices: 3904962--3905362 Score: 335
Period size: 6 Copynumber: 66.3 Consensus size: 6
3904952 CTTTTTCAAA
3904962 AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG
1 AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG
* * * * *
3905010 AATAAG GAGAAG AAGAAG GAGAAG AAGAAG GAGAAG AAGAAG GAGAAG
1 AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG
* * * * * * * *
3905058 GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG ATGAAG TAGAAG GAGAAG
1 AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG
* * * * * *
3905106 GAGAAG AAGGAAG AAGGAG AAGGAG AAGGAG AAGGAG AATG-AG AAGGAG
1 AAGAAG AA-GAAG AAGAAG AAGAAG AAGAAG AAGAAG AA-GAAG AAGAAG
* * * * * *
3905155 AAGGAG AATG-AG AAGGAG AATG-AG AAGGAG AAGGAG AATG-GG AAGGAG
1 AAGAAG AA-GAAG AAGAAG AA-GAAG AAGAAG AAGAAG AA-GAAG AAGAAG
* * *
3905203 AAGGAG AAGGAG AATG-AG AAGAAG CAGAAG AAGAAG AAGAAG AAGAAG
1 AAGAAG AAGAAG AA-GAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG
* * * * * * * * * *
3905251 AAGAAG AAGGAAG AAGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAAG
1 AAGAAG AA-GAAG AA-GAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG
* *
3905301 AAGAAG AAGCAG AAGAAG AATAAG AAGAAG AAGAAG AAGAAG AAGAAG
1 AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG
3905349 AAGAAG AAGAAG AA
1 AAGAAG AAGAAG AA
3905363 AATTTATCAA
Statistics
Matches: 355, Mismatches: 28, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
5 5 0.01
6 328 0.92
7 22 0.06
ACGTcount: A:0.56, C:0.00, G:0.42, T:0.02
Consensus pattern (6 bp):
AAGAAG
Found at i:3905481 original size:6 final size:6
Alignment explanation
Indices: 3905472--3905709 Score: 208
Period size: 6 Copynumber: 38.8 Consensus size: 6
3905462 AAGGCGTTGA
* *
3905472 AGAAGA AGAAGA AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
3905520 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGAAG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAG--G
* * * * * * * *
3905570 CAGAAGC AGAAGA AGAAGA AGAAGA AGAAAGA AGAAGA AGAAGA AGAAAG
1 -AGAAGG AGAAGG AGAAGG AGAAGG AG-AAGG AGAAGG AGAAGG AGAAGG
* * * * * * *
3905620 AGGAGG AGGAGG AGGAGG ATG-AGG AGGAGG AGGAGG AGGAGG AGGAGG
1 AGAAGG AGAAGG AGAAGG A-GAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * *
3905668 AGGAGG AGGAGG AGAATG AGGAGG AGGAAGA AGAAGA AGAAG
1 AGAAGG AGAAGG AGAAGG AGAAGG A-GAAGG AGAAGG AGAAG
3905710 AAAATTTATC
Statistics
Matches: 212, Mismatches: 13, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
5 1 0.00
6 194 0.92
7 11 0.05
8 1 0.00
9 5 0.02
ACGTcount: A:0.50, C:0.01, G:0.48, T:0.01
Consensus pattern (6 bp):
AGAAGG
Found at i:3905625 original size:3 final size:3
Alignment explanation
Indices: 3905619--3905695 Score: 127
Period size: 3 Copynumber: 25.7 Consensus size: 3
3905609 GAAGAAGAAA
*
3905619 GAG GAG GAG GAG GAG GAG GAT GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
* *
3905667 GAG GAG GAG GAG GAG AAT GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
3905696 AGAAGAAGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.35, C:0.00, G:0.62, T:0.03
Consensus pattern (3 bp):
GAG
Found at i:3907420 original size:3 final size:3
Alignment explanation
Indices: 3907412--3907458 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
3907402 GTCGTAAAAT
3907412 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3907459 GCATCTCATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3907709 original size:22 final size:22
Alignment explanation
Indices: 3907681--3907741 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
3907671 GGCATGTGAA
*
3907681 ATTTGTCCCGAAGGACCTATGT
1 ATTTGTCCCGAAGGACCTATAT
* * *
3907703 ATTTGTCCCTAATGACCTCTAT
1 ATTTGTCCCGAAGGACCTATAT
*
3907725 ATTTGTCCTGAAGGACC
1 ATTTGTCCCGAAGGACC
3907742 ACGTAGAACC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATAT
Found at i:3912036 original size:2 final size:2
Alignment explanation
Indices: 3912029--3912066 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3912019 TAATTTTCTT
3912029 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3912067 AGTTGTAAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3915121 original size:34 final size:35
Alignment explanation
Indices: 3915074--3915142 Score: 131
Period size: 34 Copynumber: 2.0 Consensus size: 35
3915064 TTCCGTTTTG
3915074 GTACTCAAATTTTAATTTTTTATTTAATATTTAAT
1 GTACTCAAATTTTAATTTTTTATTTAATATTTAAT
3915109 GTAC-CAAATTTTAATTTTTTATTTAATATTTAAT
1 GTACTCAAATTTTAATTTTTTATTTAATATTTAAT
3915143 TTAAATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 30 0.88
35 4 0.12
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.57
Consensus pattern (35 bp):
GTACTCAAATTTTAATTTTTTATTTAATATTTAAT
Found at i:3917103 original size:9 final size:9
Alignment explanation
Indices: 3917089--3917124 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
3917079 GTAATATGTT
3917089 TTTTTAATA
1 TTTTTAATA
*
3917098 TTTTTAGTA
1 TTTTTAATA
*
3917107 TTTTTTATA
1 TTTTTAATA
3917116 TTTTTAATA
1 TTTTTAATA
3917125 ATTTATTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (9 bp):
TTTTTAATA
Found at i:3921229 original size:14 final size:14
Alignment explanation
Indices: 3921212--3921242 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3921202 ATTTCTATGT
*
3921212 AGGGAATTATTTGC
1 AGGGAATTATTTAC
3921226 AGGGAATTATTTAC
1 AGGGAATTATTTAC
3921240 AGG
1 AGG
3921243 ATTACTCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.32
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:3921310 original size:4 final size:4
Alignment explanation
Indices: 3921301--3921327 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3921291 TTCATCTATG
3921301 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
3921328 ACACGCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:3922588 original size:23 final size:23
Alignment explanation
Indices: 3922559--3922602 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3922549 TTCTAATAAT
*
3922559 TTTGTCTCTATGACACATTTTTA
1 TTTGTCTCTAGGACACATTTTTA
*
3922582 TTTGTCTTTAGGACACATTTT
1 TTTGTCTCTAGGACACATTTT
3922603 CTTCTGTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.11, T:0.52
Consensus pattern (23 bp):
TTTGTCTCTAGGACACATTTTTA
Found at i:3922610 original size:23 final size:23
Alignment explanation
Indices: 3922561--3922612 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
3922551 CTAATAATTT
* * *
3922561 TGTCTCTATGACACATTTTTATT
1 TGTCTTTAGGACACATTTTTATC
3922584 TGTCTTTAGGACACATTTTCT-TC
1 TGTCTTTAGGACACATTTT-TATC
3922607 TGTCTT
1 TGTCTT
3922613 CATGGTACGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.17, C:0.19, G:0.12, T:0.52
Consensus pattern (23 bp):
TGTCTTTAGGACACATTTTTATC
Found at i:3923194 original size:14 final size:14
Alignment explanation
Indices: 3923158--3923199 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
3923148 TATATATTTT
3923158 TAATTATTTAATGAAA
1 TAATTATTTAA--AAA
3923174 TAA--ATTTAAAAA
1 TAATTATTTAAAAA
3923186 TAATTATTTAAAAA
1 TAATTATTTAAAAA
3923200 ATAGTATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 6 0.25
14 15 0.62
16 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
TAATTATTTAAAAA
Found at i:3931741 original size:23 final size:24
Alignment explanation
Indices: 3931711--3931767 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
3931701 GAGTCGAGGG
*
3931711 ATTT-ATAGTGGTCCTTCAGGAC-
1 ATTTCATAGTGGTCATTCAGGACA
*
3931733 ATTTCATAGTGGTCATTCGGGACAA
1 ATTTCATAGTGGTCATTCAGGAC-A
3931758 ATTTCATAGT
1 ATTTCATAGT
3931768 CCCTGGTGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 4 0.13
23 16 0.53
25 10 0.33
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (24 bp):
ATTTCATAGTGGTCATTCAGGACA
Found at i:3934485 original size:21 final size:21
Alignment explanation
Indices: 3934459--3934503 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3934449 GATTTCTGGG
* *
3934459 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3934480 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3934501 CAA
1 CAA
3934504 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:3935106 original size:18 final size:18
Alignment explanation
Indices: 3935083--3935117 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3935073 CTAGGAGATT
3935083 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
3935101 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
3935118 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:3935203 original size:21 final size:22
Alignment explanation
Indices: 3935174--3935217 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3935164 GTTGTATGAT
3935174 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
3935195 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
3935217 A
1 A
3935218 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:3936117 original size:149 final size:149
Alignment explanation
Indices: 3935931--3936234 Score: 554
Period size: 149 Copynumber: 2.0 Consensus size: 149
3935921 GAGTCGAGGG
3935931 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
3935996 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGAAATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGAAATCATTA
3936061 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* * *
3936080 TCTATGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
*
3936145 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGAAATCATTA
3936210 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
3936229 TCTACG
1 TCTACG
3936235 GGGCACTTCG
Statistics
Matches: 148, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 148 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGAAATCATTA
TATGGCACTACGGTGCAAT
Found at i:3936257 original size:23 final size:23
Alignment explanation
Indices: 3936213--3936257 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3936203 ATCATTATAT
*
3936213 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
3936236 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
3936258 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:3937145 original size:17 final size:17
Alignment explanation
Indices: 3937123--3937156 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3937113 AGCACACCGT
*
3937123 CATCACTCATTGTTCCC
1 CATCACTCATTCTTCCC
3937140 CATCACTCATTCTTCCC
1 CATCACTCATTCTTCCC
3937157 TTGCACATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.44, G:0.03, T:0.35
Consensus pattern (17 bp):
CATCACTCATTCTTCCC
Found at i:3944282 original size:58 final size:58
Alignment explanation
Indices: 3944180--3944293 Score: 142
Period size: 58 Copynumber: 2.0 Consensus size: 58
3944170 TATAACTCTC
* * **
3944180 ATTTTAAATTAATCCTTACACTTTTGAATGTTTAAATTATATCCCCAAACTATGTCTT
1 ATTTTAAATTAATACTTAAACTTTTGAACATTTAAATTATATCCCCAAACTATGTCTT
* *
3944238 ATTTTAAATTAGTACTTAAACTTTTGAACATTCT-AATT-TCATCCCTAAACTATGTC
1 ATTTTAAATTAATACTTAAACTTTTGAACATT-TAAATTAT-ATCCCCAAACTATGTC
3944294 CCTCTTTCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
57 1 0.02
58 46 0.96
59 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.44
Consensus pattern (58 bp):
ATTTTAAATTAATACTTAAACTTTTGAACATTTAAATTATATCCCCAAACTATGTCTT
Found at i:3944592 original size:60 final size:59
Alignment explanation
Indices: 3944461--3944652 Score: 196
Period size: 60 Copynumber: 3.2 Consensus size: 59
3944451 GTATATACAT
* * *
3944461 ATAGTTTGAGATGAAATT-AGAATGTTCAAAAAGTTT-GGGGACCAATTTAGAATGAATGTC
1 ATAGTTTGGGATGAAATTGA-AATGTTC-AAAAGTTTAAGGG-CTAATTTAGAATGAATGTC
*
3944521 ATAGTTTGGGATGAAATTGAAATGTTCAAAAGTTTAAGGGCTAATTTAGACTG-ATAGTC
1 ATAGTTTGGGATGAAATTGAAATGTTCAAAAGTTTAAGGGCTAATTTAGAATGAAT-GTC
* * **
3944580 ATAGTTTAGGGATGAAATTGGAACAT-TT-AAAAGTTTAAGGACTAATTTAAAATGAGGGTC
1 ATAGTTT-GGGATGAAATT-GAA-ATGTTCAAAAGTTTAAGGGCTAATTTAGAATGAATGTC
*
3944640 ATACTTTGAGGAT
1 ATAGTTTG-GGAT
3944653 ATATGTTGTA
Statistics
Matches: 114, Mismatches: 10, Indels: 16
0.81 0.07 0.11
Matches are distributed among these distances:
58 2 0.02
59 30 0.26
60 74 0.65
61 6 0.05
62 2 0.02
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (59 bp):
ATAGTTTGGGATGAAATTGAAATGTTCAAAAGTTTAAGGGCTAATTTAGAATGAATGTC
Found at i:3945041 original size:24 final size:23
Alignment explanation
Indices: 3944989--3945042 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
3944979 TATTTTTCTA
* *
3944989 ATAATTTAACAAAAAATAGTTTT
1 ATAATTTAACAAAAAATAATTTC
*
3945012 AAAATTTAA-AAACGAAATAATTTC
1 ATAATTTAACAAA--AAATAATTTC
3945036 ATAATTT
1 ATAATTT
3945043 TGTTATAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 3 0.12
23 8 0.32
24 14 0.56
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (23 bp):
ATAATTTAACAAAAAATAATTTC
Found at i:3957013 original size:11 final size:12
Alignment explanation
Indices: 3956988--3957020 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3956978 CTTATAGATA
3956988 TTAAATTACATT
1 TTAAATTACATT
*
3957000 TTACATTA-ATT
1 TTAAATTACATT
3957011 TTAAATTACA
1 TTAAATTACA
3957021 CTTCCATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (12 bp):
TTAAATTACATT
Found at i:3957037 original size:23 final size:23
Alignment explanation
Indices: 3956985--3957038 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
3956975 AATCTTATAG
*
3956985 ATATTAAATTACATTTTACATTA
1 ATATTAAATTACATCTTACATTA
* *
3957008 ATTTTAAATTACA-CTTCCATTA
1 ATATTAAATTACATCTTACATTA
3957030 TATATTAAA
1 -ATATTAAA
3957039 CAATTGATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (23 bp):
ATATTAAATTACATCTTACATTA
Found at i:3959650 original size:16 final size:16
Alignment explanation
Indices: 3959629--3959666 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
3959619 GTACTTTCAA
3959629 AATTTTAATTTATTTT
1 AATTTTAATTTATTTT
3959645 AATTTTAATTTATTTT
1 AATTTTAATTTATTTT
3959661 AATTTT
1 AATTTT
3959667 TTTCATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTTTAATTTATTTT
Found at i:3963570 original size:43 final size:43
Alignment explanation
Indices: 3963509--3963664 Score: 125
Period size: 43 Copynumber: 3.4 Consensus size: 43
3963499 CAGAGCCAAT
3963509 TTCAACTTCAC-AGCGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACGA-CGAAGGATATTGGACTCCAGACAACGCAAG
*** ** * * * *
3963552 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
1 TTCAACTTCACGACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
* *
3963603 TTCAACTTCGCAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGCAAG
3963646 TTCAACTTCACGACGAAGG
1 TTCAACTTCACGACGAAGG
3963665 GACCGCTGGT
Statistics
Matches: 82, Mismatches: 22, Indels: 18
0.67 0.18 0.15
Matches are distributed among these distances:
43 36 0.44
44 4 0.05
45 3 0.04
46 7 0.09
48 7 0.09
49 3 0.04
50 3 0.04
51 19 0.23
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGCAAG
Done.